diff mbox series

[bug#65364] gnu: Add python-scDamAndTools.

Message ID fa8a55823ad0ad4f36c81fb7d6957a80f85d434a.1692367266.git.navid.afkhami@mdc-berlin.de
State New
Headers show
Series [bug#65364] gnu: Add python-scDamAndTools. | expand

Commit Message

nafkhamdc Aug. 18, 2023, 2:01 p.m. UTC 
* gnu/packages/bioinformatics.scm (python-scDamAndTools): New variable.
---
 gnu/packages/bioinformatics.scm | 34 +++++++++++++++++++++++++++++++++
 1 file changed, 34 insertions(+)


base-commit: 1b2d43fe016848ea2ec16ff18cbc14340944fc4e

Comments

Ricardo Wurmus Aug. 28, 2023, 7:51 a.m. UTC | #1 
Thanks for the patch.  I renamed it to all lowercase and changed the
description a little bit.

Pushed!
diff mbox series

Patch

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 51640b710f..03b1e81634 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -2154,6 +2154,40 @@  (define-public python-pybedtools
     ;; licensed lgpl2.1+
     (license (list license:expat license:lgpl2.1+))))
 
+(define-public python-scDamAndTools
+  (package
+    (name "python-scDamAndTools")
+    (version "1.0")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/KindLab/scDamAndTools")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "1mblw6cn5jqik6ky8cv7ry99z6jm1i4r71pzdfl398vrwbda65gd"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list #:tests? #f)) ;there are none
+    (propagated-inputs (list python-h5py
+                             python-numpy
+                             python-sortedcontainers
+                             python-pandas
+                             python-pysam
+                             python-tqdm))
+    (native-inputs (list python-cython python-pytest))
+    (home-page "https://github.com/KindLab/scDamAndTools")
+    (synopsis "Functions for processing raw scDam&T-seq data")
+    (description
+     "This is a set of unctions for processing raw scDam&T-seq data.
+A method to simultaneously measure protein-DNA interactions and transcription
+from single cells (Rooijers et al., 2019). scDam&T-seq combines a DamID-based
+method to measure protein-DNA interactions and an adaptation of CEL-Seq to
+measure transcription.  The starting point of the workflow is raw sequencing
+data and the end result are tables of UMI-unique DamID and CEL-Seq counts.")
+    (license license:expat)))
+
 (define-public python-bioframe
   (package
     (name "python-bioframe")